New Windows Version 7 Features

FlowJo is like the Swiss army knife of Flow Cytometric analysis programs. It contains tools for all of the jobs you need to easily and efficiently perform any type of data analysis from start to finish. For detailed release notes through v. 5.7.1, CLICK HERE.

Index:
Version 7.2.5 (April 6, 2008)
Version 7.2.4 (February 27, 2008)
Version 7.2.2 (June 6, 2007)
Version 7.2 (February 8, 2007)
Version 7.1.3 (October 9th 2006)
Version 7.1.2 (August 3rd 2006)
Version 7.1.1 (July 5th 2006)
Version 7.1.0 (May 17th 2006)
Version 7.0.6 (April 28th 2006)

• April 6th 2008, Version 7.2.5 release
• "out of memory" errors were addressed by better defaults
  
• authorization fixes for consistent hardware addresses (Nortel adapters)
• bug fix for printing contents of workspace
• authorization fix when multiple USB thumbdrives are attached

• February 27th 2008, Version 7.2.4 release
  
• One version now runs on Win2000/XP/Vista
• Compatible with new and old black dongles

• June 6th 2007, Version 7.2.2 release
  Known Issues:
• calibration from V5 and early V7 workspaces should be recalculated
• the "custom label" visible in table editor when nodes are dragged into the table editor should not be used in creating formulae. Instead, type over them with your own (ergo, custom) labels and use those.
  
• windows 64 bit does not work with serial numbers yet.
  
• file export ignores custom keywords
  Fixed since 7.2.1:
  Authorization:
  
• proxy support for site license holders has been fixed (sorry for the delay!)
  
• full S/N or dongle, About FJ displayed DEMO mode.. fixed
  
• added Vista support (dongles, serial numbers, FLS, proxy)
  
• added partial win xp 64 bit support (see Known Issues..)
  GW:
  
• rect gate is offset by 10 pixels when first created).
  
• bug where output to pdf/svg did not work in graph window and layout editor.
  
• Open saved WS with a GW(s) will indicate it's been edited.
  
• conceptual problem with implementation of bisector gate
  
• Invalid Not Gate - would make a gate higher than 100 %
  
• toggling gate 'events inside' changed the gate coordinates.
  
• X or Y axis is changing after graph type is changed.
  
• Ellipse gates from older workspaces would not calculate the right frequencies.
  Table Editor:
  
• Formula for Quad gates not adding up to 100 percent
  
• error message popped up sometimes on table selection
  
• fixed error where -1 would show as a stat for empty gates
  
• some stats will now be shown as "N/A" vs. 0 where appropriate
  
• fixed table sorting
  FCS spec:
  
• Fixed logic in Sample.createBeckmanCoulterCompMatrix.
  
• Allow compensation on SSC-W parameter when it's index is greater than 3, to support old cellquest machines where ssc-w was used as a fluorescent channel.
  Layout:
  
• keyword/discriminator iteration did not work for templates.
  
• Batching to PDF would not iterate annotation for some of the charts
  
• error messages pop up in old layouts
  
• grid behavior improved on re-opening saved WS's
  
• After batched to PDF page brake returned to default setting. fixed.
  
• There was a problem with overlay in V 7.2.1, fixed.
  
• Edit menu Edit Chart fails to de-select the chart option
  
• stat nodes in LE need "gating path" option
  
• new: adjunct histograms. Drag a chart to LE, right click, add adjunct histo's.
  Workspace:
  
• Files would not load after Reset to Defaults in Prefer. using a S/N
  
• added a need a global preferences reset button
  
• Renaming samples was no longer possible
  
• added 'Alt Preferences' option
  
• Stat node "Freq of Parent" was not the same as gate node
  
• Stat "Freq of Parent" failed to track/update with gate node after quad gate was moved
  
• DiVa sample stain name didn't carry forward to new parameter
  
• combination boolean gates are now calculating right cell counts
  
• fixed compatibility of 5.7.2 workspace
  
• new private pref: private_writeAbsoluteFilePath, when set to ="1" in your flowjo7.prefs file, will create absolute paths (ex. c:\user\data\file.fcs)
  Platforms:
  
• fixed ability to make manual timeslices in kinetics
  
• calibration works!
  
• e-added support for kinetics node overlays
  
• compensation and calibration parameters will be auto-added to group upon their creation
  
• V7 on OSX:
• quicktime movies broken if V7 runs on mac


• February 8th 2007, Version 7.2 release
  Authorization:
  
• FLS lookup should be much more rapid now
  
• different demo serial numbers will be issued starting 7.2 release
  
• serial number fields will show the "paste" menu when clicked
  
• fixed the problem with multiple hardware addresses, licensing via serial number should be easier.
  Buttons and menus:
  
• "quit" button would ignore changes in FJ License Info dialog. Fixed.
  Compensation:
  
• added compensation scripting. Explained here.
  Diva:
  
• diva data from 3.1, 4.0, or 4.0.1 will be compensated properly
  
• we're no longer transforming linearly scaled diva parameters.
  
• DiVa prefs are now embedded into workspace files, and will over-ride local prefs if different.
  
• fixed problem with opening large diva files (tested up to 2.5M events)
  Graph Window:
  
• gate freq. positioning and color inconsistent - fixed.
  
• dragging gates around would sometimes put some vertices off-screen. fixed.
  
• implemented polygon gate editing - alt+click = delete ctrl+alt = duplicate
  
• added keyboard shortcut ctrl+shift+r - resets all graph window sizes to one size.
  
• fixed the bug which made some windows oblong and warped.
  
• stats area now has scrollbars
  
• added ability to control fill setting in the histogram thru right-click menu
  
• added ability to copy histogram data as scale or channel values.
  
• preferences window painted in the wrong layer. Could lead to GUI block. Fixed.
  
• gating tools have keyboard shortcuts: (q)uad, (s)elect, (e)lipse, (r)ectangle, (p)olygon. In histogram mode, Q- bisecotor and I- range gate.
  
• double click gating tools to make them "stick" (draw other gates)
  
• fixed ellipse gates
  
• no more PINK gates. default changed to BLACK.
  Kinetics
  
• KI fixed all kinds of kinetics bugs (FCS3 and FCS2 files, scaling, plotting, stats vs. mac)
  Layout Editor
  
• dotting and dashing quality for overlay plots, lines, arrows, etc..
  
• overlay UI enhancements in the legend of overlays in layouts
  
• last layout is not deletable
  
• erratic change of sample selection in the layout
  
• sometimes gates would become extra-highlighted for no reason.. fixed.
  
• layouts with iteration errors would sometimes display a blank box without explaining.. fixed.
  
• chart duplication resulted in dragging chart without annotation. fixed.
  
• fixed series of bugs with multi-graph overlays. Added kb shortcut ctrl+shift+M to add graph.
  
• re-opened workspaces with batched layout would show the same stats or keywords.. fixed.
  
• saving to PDF fixed from layouts. PDF's will now use layout's pagination.
  
• batch dialog now remembers settings for each output when you switch output options
  
• printing dotplots with frequency floaters would make floaters unreadable.. fixed
  
• creating an oval gate in LE would put FlowJo in a weird state. fixed.
  
• improved gate editing UI - reduced number of mouse clicks in gate editing to 1
  
• fixed unit distribution axis lables to be independent of sigFigs setting
  
• fixed overlay line attribute bug
  
• legend-set controls are more consistent
  
• legend widths are now dynamically updated to fit content
  
• X axis label will now properly move closer if "hide numbers" checked in Graph Def'n dialog.
  
• saving textbox commits contents to become default annotation for graphs.. fixed.
  
• added rightclick menu which makes certain menu items easier to access (ie. paste)
  
• moving a gate in LE would snap the gate back.. fixed.
  
• added "set control" to right-click legend menu
  
• rightclick on chart shows parameters with current parameter grayed out.
  
• layout would not allow overlaying the same gate over itself, fixed.
  
• enabled gating to work properly in "graph sets"
  
• new zoom tool - left to the old one - allows drawing a rect-selection of what to zoom in on
  
• fixed header/footer
  
• implemented autobatching of layouts
  Plate Editor
  
• fixed file menu items
  Preferences
  
• disabled changing $FIL by renaming sample
  
• added pref for linear FL channel scaling for DiVa parameters
  
• added ability to save prefs for legend styling: line thickness, columns, colors..
  
• if flowjo diva scaling options are in effect, they will now take priority over $PNdisplay kw
  
• FlowJo's got a new private preference, private_showStainInStatisticsDialog. Set it to ="1" or "0" to toggle display of prefs with/out stain names (ex. fitc-a vs. fitc-a CD3)
  
• deleting a gate from favorites would corrupt remaining gates into a single-string.. fixed
  
• added right-click "paste" operation to serial number fields ;)
  
• added 32 bit (DIVA etc.) prefs link under Edit menu
  Table Editor
  
• TE added shortcut to graph window (double-click on a row)
  
• can now move columns (drag column header to re-arrange output)
  
• added "copy raw" and "html" flavors to the clipboard
  
• can now set "clipboard" as an output option for generating tables
  
• can now "hide" output columns (double-click on an item in editor to enable attribute)
  Workspace
  
• boolean gate's children nodes would sometimes calculate wrong %, fixed.
  
• boolean gates would misbehave when parent gates renamed
  
• nested boolean gates and their NOT gates would misbehave.. fixed
  
• group owned gates are no longer rename-able (have to detach it from group, then rename it)
  
• added support for the coulter CXP FCS3 format ($DFC...) - this needs verification
  
• closing workspace while adding samples would cause an error. Fixed.
  
• entering a "/" character into file name during save operation would nullify the save, fixed.
  
• deleting a compmatrix now properly un-compensates files in WS view.
  
• changing group name resets gate styling.. fixed
  
• can add multiple keywords in one shot
  
• added support for relative URI's if workspace is in parent folder relative to data.
  
• when editing keywords, users can now go across (tab) or down (enter)
  
• FCS and CSV data export as well as FCS concatenation have been fixed.
  
• ability to copy spreadsheets into flowjo to label keyword values has been added.
  
• ability to export csv files with gate inclusion/exclusion per event info added.
  
• can now drag files from one workspace window to another. gates, too.
  
• calibrated parameters did not work before. They work now.

• October 9th 2006, Version 7.1.3 released
  
  
• Better error message when dropping control populations in the drop boxes of the compensation editor.
  
• Better retention of drop boxes in the compensation editor when performing editing operations.
  
• FlowJo now recognizes SPILL keyword if the parameter has a '/' in the name.
  
• Cell cycle platform now shows displays better warnings and the mouse tracker matches the axes values.
  
• New operations were added to allow user to specify gate color and line thickness, to apply these to other gates, and to save as a preference.
  
• Ellipse gates no longer shift slightly when using the arrow keys to move then, due to rounding errors.
  
• Can now display large dots for pseudo-color graphs.
  
• Much improved output of pdf, svg, gif in the layout editor.
  
• Can now delete the legend in the layout editor by selecting it and hitting the delete key.
  
• New y-axis option for histogram overlays: Unit Distribution, which normalizes the area under the curves to 1.
  
• Correct display of histogram overlays with a postive offset (angled view).
  
• Correct clipping of histogram overlays when copying them to the clipboard.
  
• Can now save the position and properties of legends and annotations as a preference for the layout editor.
  
• And/Or gates correctly determine their parentage when copied to another location.
  
• Export gated subpopulation to new FCS files.
• Concatenate samples or other populations to new FCS files.
• Added scrollbars to popup menu in graph window to choose sibling populations.
• Added menu operation to apply modifications to group-owned gates.
• Added new functionality to auto-batch multiple layouts in one operation.
• Improved memory deallocation when a workspace is closed.
• Added experiment ID support.
• Added support for black dongles when running v7 on Mac.
• Added crash protection for engine requests (i.e. no more hard crashes.)
• Added XML validation prior to save.
  

• August 3rd 2006, Version 7.1.2 released
  
  
• Workspaces with many gates should experience large performance improvements.
  
• Multiple bugs in DiVa and non-DiVa transformation have been fixed.
  
• Default global transform settings are now more reasonable.
  
• DiVa linear parameters and scaling now more closesly match DiVa software.
  
• Manual editing of cell cycling and proliferation platforms have been improved.
  
• Several bugs in proliferation have been fixed.
  
• Kinetics and proliferation graphs now dynamically update in the layout editor.
  
• Calibration works correctly again.
  
• All layout editor iteration options now work correctly for workspaces and templates.
  
• Batching to separate pages has been fixed.
  
• Printing has had several fixes, especially for headers and footers.
  
• Exporting layout graphics to other applications now has correct scaling and better naming.
  
• Version 8 (Macintosh) compensation matrices should now all be read correctly.
  
• A number of bugs where preferences were not being remembered correctly have been fixed.
  
• Combination gates have had several important bug fixes.
  
• The table editor and its formulas have had several bugs fixed.
  
• Very large statistical and tabular values sometimes have their highest digits truncated. This has been fixed.
  
• New menu item, 'Recalculate Gates and Statistics', is now available.
  
• Quad gates not adding up to 100% should now all be fixed. Use the recalculate menu item if necessary on older workspaces.
  
• Quad annotations may now be kept in the corners using a preference.
  
• New predefined values, 'Graph Spec' and 'Gate Coordinates', may now be added as workspace columns.
  
• Parameters named with forward slashes could cause problems when gating. This has been fixed.
  
• A bug in ratio derived parameter was fixed.
  
• Lines drawn in the layout editor now are at right angles when shift is held.
  
• Multiple acquisition related enchancements have been added.
  
• Users of older dongles may now force the upgrade process to happen by holding shift and control and clicking 'About Dongles' in the license information window.
  
• If a user is in demo mode, this is displayed on the about window.
  
• Release notes are now visible through the workspace help menu.
  
• Many help links have been corrected.
  
• Several additional, miscellaneous bugs have been fixed.

July 5th 2006, Version 7.1.1 released

• Considerable optimizations have been made to the internals of FlowJo to provide much better performance when analyzing large, complex data sets.
• Numerous bugs with resizing charts and other figs in the layout editor have been fixed.
• Batching direct to printer no longer has an arbitrary limit to the number of tiles per page.
• Percentile statistics in table outputs were sometimes incorrectly displaying zeros. This has been fixed.
• There is a new 'Report Bug' menu item under the 'Help' menu that presents the new bug reporting web page at http://umpqua.treestar.com/ bugs/ .
• When creating new gates, the stain name (if available) is now used for the default name instead of the parameter name.
• Compensation matrices that differ by only 0.01 (settable as a preference) or less are now treated as the same matrix.
• It is now possible to edit the properties of multiple charts in the layout editor at once. This is done by selecting all the charts to edit and then displaying the properties of one of them. Changes are then propagated to all the selected charts.
• Although functionally correct, transform vectors being calculated did not distribute the events across the negative range similarly to the Mac version. This has been changed to match the Mac version's behavior which produces better transformations with more optimal clustering.
• Quad gate annotations in older templates and workspaces sometimes would return to their original positions even after being repositioned when the quad gate was moved. Enabling the 'private_quadAnnotationsInCorner' preference now keeps quad gate annotations in the corner.
• Quad gates are no longer separable.
• A 'pause' button has been added to the gate editing tool bar in the layout editor. When pressed, the pause button delays applying editing changes (e.g. moving a gate) to other parts of the program.
• Parent graphs displayed by showing ancestry in the layout editor now only show the gate that applies to the child graph.
• When using text boxes in the layout editor which were opened from a template, problems could arise where the FJML tags (such as a keyword of the current sample) would not display incorrectly. These problems have been fixed.
• Compensation matrices in Summit 4.2 and 4.3 are now being read correctly. Due to changes between Summit versions, there were problems previously.
• 'FS Lin', 'SS Lin', 'FS Log' and 'SS Log' are now correctly treated as non-fluorescent parameters.
• Global DiVA settings were overriding template's transform settings. This has been fixed. Additionally, the global DiVa settings dialog has been enabled again.
• In the case where a sample file could not be read correctly (e.g. disk error), an endless loop was occurring which would cause an exception. This has now been fixed.
• Generated tables weren't using the formatting criteria correctly. This has been fixed.
• Some groups weren't being saved in templates. This has been fixed.
• Notification for when a new version has been improved so beta versions do not erroneously display 'New Version Available' messages.
• Several optimizations to performance have been added.

May 17th 2006, Version 7.1.0 released

• Show Backgating command in the Layout editor now displays a legend identifying parameters on each graph.
• When creating histogram overlays in the Layout Editor, right click for a new option to normalize the area under the curves.
• Histograms in the layout editor can be smoothed incrementally by right clicking and selecting Smooth.
• Change graph type and other options on multiple graphs in the layout editor by right clicking and selecting the desired options.
• Derived Parameters have their own dialog box. Reach it by right clicking on the sample in the workspace or select Derived Parameters from the Tools menu.
• Save the current state of a tool set-up by selecting Save State to Preferences in the EDIT menu. This is now available in the Workspace, Graph Window, Sayout Editor and when batching.
• OR gates and AND gates now reload correctly from saved workspaces.
• You can no longer overlay populations with different transformation settings.
• Quad Gates displaying frequency and gate names now retain their labels properly.
• Quad gates can now be nudged using the arrow keys.

April 28th 2006, Version 7.0.6 released

• New Autogating tool implemented in Graphs and Layout.
• Transformation panel adds global manipulation for Transformation settings and their application to tubes and groups. View, create, edit and remove settings, specify automatic or manual calculation for extra negative decades.
• Batch Layout to PowerPoint and PDF.
• Greatly improved batch performance.
• Improved global text trait controls.
• Faster printing.
• Supports password protected proxy servers.
• Large dots available on graphs in Graph Window and Layout Editor.
• Numerous bug fixes.

Web Start.  Allows us to deploy improvements in small chunks. When you start FlowJo it will check for updates and download them. You will always have the most current version. Get it from the Download Page.

Experiment Annotator   Clinical sites and high throughput research labs need to improve levels of automation to significantly decrease repetitive tasks, and enable large scale tests.  FlowJo’s Experiment Annotator is a 96 well plate editor for describing staining setup using attribute - value pairs.  The Experiment Annotator enables creation and editing of samples prior to collection.  It is also a means to editing sample descriptions after collection.

Graph Windows  Resizable graph windows are available in 7.0 for your personal dimensioning preference.  Gate calculation has been optimized, and statistics may be added to all parameters.  The gate creation window has the capability to retrieve gate names by way of an editable favorites list accessible during gate creation. 

Layout Editor It is possible now to save/load graph setups from Multigraph overlay to graphs in the layout editor.  Percentile gating is also available:  a percentile gate may be applied to another population, the absolute position of the gate may differ, but the percentage of events within the gate matches that originally defined.

Preferences  Templates and workspaces are now delivered with preferences set.  A workspace may contain a preference element, or any subset of the elements and attributes supported in FlowJo.   The setting and saving of preferences is primarily accomplished locally to each menu.  On exit, workspace, templates and layouts carry their font information with them.

Workspace  Group analysis gate calculations are now activated on-demand resulting in an overall performance optimization.  Group functionality has been enhanced for gate creation and renaming.  Synchronized groups enable the automation of application of gates across a selection of samples.   Become a 7.0 beta tester, and let us work with you on your personal wish list.  Have a go at the 7.0 workspace, there are various other enhancements with respect to your statistical analyses: concatenate and export FCS files to extend your raw data file selection; quickly access your 10 most recent workspaces; ongoing 32 bit data analysis capability; display a  numerical series with a click of a keyword value… and more.

Table Editor  The Table Editor has had many improvements expanding its functionality and integration within an organization.  Advanced batching capability has been added, allowing you to create tables that intelligently combine multiple samples into single table rows.   A powerful new formula engine is now available to programmatically produce columns providing a wide range of statistical, mathematical and textual operations.  Flexible formatting settings have been added to give your tables a customized look and you can drag and drop these formatted tables directly into Microsoft Word, Excel and other programs.  New export formats have been added: Native Excel, Excel XML, Open Document XML, CSV, HTML and RTF.  You can also export into an SQL-92 script, providing a direct path for putting your tables into most databases.  All exports can be done directly to an FTP site as well as to a local file.  And, all of these new features may be combined into templates with one-click table creation and output.

Compensation/Transformation   A new streamlined user interface enables ease of compensation and transformation analyses, as well as computations using derived parameters.  The new, more intuitive approach to compensation features single step creation of the compensation matrix.

Performance  A more finely tuned FlowJo engine has introduced a new level of efficiency in batching sizable analyses.  Next time you run a batch from the layout, we hope you will take the opportunity to give us your feedback.

Multigraph Overlay  Multigraph Overlay is now available through the Layout Editor.  It is now possible to transform a graph in the Layout Editor to a Multigraph overlay, add a graph to the Multigraph overlay, and revert back to separate graphs, batch the overlay, save and reload.

Backgating Analysis Validating gate positions is one of the most important aspects of multiparameter Flow Cytometry. FlowJo now provides you with a tool to view the effect of every gate on your final gated population! In the Layout Editor, for any graph of a subset that is gated more than once, you can right-click and select Show Backgating from the pop-up menu.  FlowJo displays a series of graphs where each level in the gating hierarchy is displayed, with the final gated population overlaid at each level. This overlay shows what the final gated population would look like within the context of the larger population. Therefore, you can quickly scan to see if any one of your gates is positioned incorrectly. The backgating display can be printed and copied. 

Boolean Gates  You can now create a gate which is a Boolean combination of any existing gates (i.e., "and", "or", and "not" combinations). Boolean gates are "live", meaning that they will reflect any changes to the gates on which they depend, with a double- click to the gate in the workspace. FlowJo can also automatically create a series of Boolean gates that represent all combinations (plus and minus) of a set of gates. For example, if you have a sample which was stained on different parameters for IL2, TNF, and IFNg, you can create a positive gate for each of the three cytokines (for example, a histogram gate). To create or edit Boolean gates, choose the parent subset(s) and select the type of gate you need from the Workspace menu. To view the whole Boolean series, select Create combination gates...

Data Movies  You may now observe your samples as a QuickTime movie. This enables analyses to be viewed in a real-time as an animation or by stepping through frames one at a time for a more careful examination of samples.  Access this feature from any Graph Window’s “Graph” pull down menu.